HEADER OXIDOREDUCTASE/DNA 29-NOV-07 3BI3 TITLE X-RAY STRUCTURE OF ALKB PROTEIN BOUND TO DSDNA CONTAINING 1MEA/A WITH TITLE 2 COFACTORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC REPAIR DOMAIN; COMPND 5 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*TP*AP*GP*GP*TP*AP*AP*(MA7)P*AP*(2YR)P*CP*GP*T)- COMPND 11 3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'- COMPND 16 D(*DAP*DAP*DCP*DGP*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3'); COMPND 17 CHAIN: C; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: ALKB, AIDD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS DIOXYGENASE, PROTEIN DNA INTERACTION, ALKYLATION REPAIR, DNA DAMAGE, KEYWDS 2 DNA REPAIR, IRON, METAL-BINDING, OXIDOREDUCTASE, OXIDOREDUCTASE-DNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.YI,C.-G.YANG REVDAT 7 30-OCT-24 3BI3 1 REMARK REVDAT 6 20-OCT-21 3BI3 1 REMARK SEQADV LINK REVDAT 5 21-MAY-14 3BI3 1 COMPND REMARK SEQRES HET REVDAT 5 2 1 HETNAM FORMUL LINK SITE REVDAT 5 3 1 HETATM ATOM REVDAT 4 13-JUL-11 3BI3 1 VERSN REVDAT 3 24-FEB-09 3BI3 1 VERSN REVDAT 2 10-JUN-08 3BI3 1 JRNL REVDAT 1 22-APR-08 3BI3 0 JRNL AUTH C.G.YANG,C.YI,E.M.DUGUID,C.T.SULLIVAN,X.JIAN,P.A.RICE,C.HE JRNL TITL CRYSTAL STRUCTURES OF DNA/RNA REPAIR ENZYMES ALKB AND ABH2 JRNL TITL 2 BOUND TO DSDNA. JRNL REF NATURE V. 452 961 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18432238 JRNL DOI 10.1038/NATURE06889 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 20726 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1114 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1263 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.2340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1572 REMARK 3 NUCLEIC ACID ATOMS : 515 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 168 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.14000 REMARK 3 B22 (A**2) : -2.55000 REMARK 3 B33 (A**2) : 4.65000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.191 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.164 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.117 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2247 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3163 ; 1.093 ; 2.254 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 208 ; 5.651 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;35.257 ;23.038 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 257 ;12.089 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;15.316 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 335 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1605 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 937 ; 0.175 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1420 ; 0.299 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 198 ; 0.097 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 32 ; 0.090 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.106 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1057 ; 0.279 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1661 ; 0.459 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1532 ; 0.643 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1502 ; 1.150 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 13 A 213 REMARK 3 ORIGIN FOR THE GROUP (A): -6.5917 1.7121 -23.2903 REMARK 3 T TENSOR REMARK 3 T11: -0.1581 T22: -0.1479 REMARK 3 T33: -0.1743 T12: -0.0012 REMARK 3 T13: -0.0212 T23: 0.0171 REMARK 3 L TENSOR REMARK 3 L11: 2.2419 L22: 2.5970 REMARK 3 L33: 0.5785 L12: -0.1061 REMARK 3 L13: -0.3796 L23: 0.4873 REMARK 3 S TENSOR REMARK 3 S11: -0.0304 S12: 0.0560 S13: 0.1167 REMARK 3 S21: -0.1516 S22: 0.0229 S23: 0.0618 REMARK 3 S31: -0.0290 S32: 0.0066 S33: 0.0075 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3BI3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045548. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24645 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 8K, 100 MM SODIUM REMARK 280 CHLORIDE, 25 MM MAGNESIUM CHLORIDE, 0.1M CACODYLATE, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 37.81450 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4280 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 DT B 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DA B 6 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DG C 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT C 6 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA C 7 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT C 8 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 DA C 10 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DC C 11 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 14 97.03 -67.94 REMARK 500 ARG A 24 18.82 59.81 REMARK 500 ILE A 201 -72.40 67.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 131 NE2 REMARK 620 2 ASP A 133 OD1 96.2 REMARK 620 3 HIS A 187 NE2 94.0 93.5 REMARK 620 4 AKG A 302 O2 98.6 104.4 156.7 REMARK 620 5 AKG A 302 O5 90.8 171.7 90.4 70.0 REMARK 620 6 HOH A 427 O 174.1 89.7 86.4 79.1 83.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FD8 RELATED DB: PDB REMARK 900 THE SAME PROTEIN REMARK 900 RELATED ID: 2BHZ RELATED DB: PDB REMARK 900 HOMOLOG REMARK 900 RELATED ID: 2IUW RELATED DB: PDB REMARK 900 HOMOLOG REMARK 900 RELATED ID: 3BHZ RELATED DB: PDB DBREF 3BI3 A 13 213 UNP P05050 ALKB_ECOLI 13 213 DBREF 3BI3 B 1 13 PDB 3BI3 3BI3 1 13 DBREF 3BI3 C 1 13 PDB 3BI3 3BI3 1 13 SEQADV 3BI3 CYS A 129 UNP P05050 SER 129 ENGINEERED MUTATION SEQRES 1 A 201 GLU PRO LEU ALA ALA GLY ALA VAL ILE LEU ARG ARG PHE SEQRES 2 A 201 ALA PHE ASN ALA ALA GLU GLN LEU ILE ARG ASP ILE ASN SEQRES 3 A 201 ASP VAL ALA SER GLN SER PRO PHE ARG GLN MET VAL THR SEQRES 4 A 201 PRO GLY GLY TYR THR MET SER VAL ALA MET THR ASN CYS SEQRES 5 A 201 GLY HIS LEU GLY TRP THR THR HIS ARG GLN GLY TYR LEU SEQRES 6 A 201 TYR SER PRO ILE ASP PRO GLN THR ASN LYS PRO TRP PRO SEQRES 7 A 201 ALA MET PRO GLN SER PHE HIS ASN LEU CYS GLN ARG ALA SEQRES 8 A 201 ALA THR ALA ALA GLY TYR PRO ASP PHE GLN PRO ASP ALA SEQRES 9 A 201 CYS LEU ILE ASN ARG TYR ALA PRO GLY ALA LYS LEU CYS SEQRES 10 A 201 LEU HIS GLN ASP LYS ASP GLU PRO ASP LEU ARG ALA PRO SEQRES 11 A 201 ILE VAL SER VAL SER LEU GLY LEU PRO ALA ILE PHE GLN SEQRES 12 A 201 PHE GLY GLY LEU LYS ARG ASN ASP PRO LEU LYS ARG LEU SEQRES 13 A 201 LEU LEU GLU HIS GLY ASP VAL VAL VAL TRP GLY GLY GLU SEQRES 14 A 201 SER ARG LEU PHE TYR HIS GLY ILE GLN PRO LEU LYS ALA SEQRES 15 A 201 GLY PHE HIS PRO LEU THR ILE ASP CYS ARG TYR ASN LEU SEQRES 16 A 201 THR PHE ARG GLN ALA GLY SEQRES 1 B 13 DT DA DG DG DT DA DA MA7 DA 2YR DC DG DT SEQRES 1 C 13 DA DA DC DG DG DT DA DT DT DA DC DC DT MODRES 3BI3 MA7 B 8 DA 1N-METHYLADENOSINE-5'-MONOPHOSPHATE HET MA7 B 8 22 HET 2YR B 10 22 HET MN A 301 1 HET AKG A 302 10 HETNAM MA7 1N-METHYLADENOSINE-5'-MONOPHOSPHATE HETNAM 2YR 2'-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 2YR PHOSPHATE) HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 2 MA7 C11 H17 N5 O6 P 1+ FORMUL 2 2YR C11 H18 N3 O7 P S FORMUL 4 MN MN 2+ FORMUL 5 AKG C5 H6 O5 FORMUL 6 HOH *168(H2 O) HELIX 1 1 ALA A 29 SER A 42 1 14 HELIX 2 2 PRO A 93 ALA A 107 1 15 HELIX 3 3 GLY A 179 ARG A 183 5 5 SHEET 1 A 7 PRO A 14 ALA A 16 0 SHEET 2 A 7 ALA A 19 LEU A 22 -1 O ALA A 19 N ALA A 16 SHEET 3 A 7 VAL A 175 TRP A 178 -1 O VAL A 175 N LEU A 22 SHEET 4 A 7 ILE A 143 GLY A 149 -1 N ILE A 143 O TRP A 178 SHEET 5 A 7 ARG A 204 ARG A 210 -1 O PHE A 209 N VAL A 144 SHEET 6 A 7 ALA A 116 TYR A 122 -1 N TYR A 122 O ARG A 204 SHEET 7 A 7 ALA A 60 CYS A 64 -1 N THR A 62 O ILE A 119 SHEET 1 B 2 GLY A 68 HIS A 72 0 SHEET 2 B 2 GLY A 75 SER A 79 -1 O SER A 79 N GLY A 68 SHEET 1 C 4 LEU A 128 HIS A 131 0 SHEET 2 C 4 HIS A 187 ILE A 189 -1 O ILE A 189 N LEU A 128 SHEET 3 C 4 ALA A 152 PHE A 156 -1 N GLN A 155 O GLY A 188 SHEET 4 C 4 LYS A 166 LEU A 170 -1 O LEU A 168 N PHE A 154 LINK SG CYS A 129 S 2YR B 10 1555 1555 2.04 LINK O3' DA B 7 P MA7 B 8 1555 1555 1.60 LINK O3' MA7 B 8 P DA B 9 1555 1555 1.60 LINK O3' DA B 9 P 2YR B 10 1555 1555 1.60 LINK O3' 2YR B 10 P DC B 11 1555 1555 1.60 LINK NE2 HIS A 131 MN MN A 301 1555 1555 2.17 LINK OD1 ASP A 133 MN MN A 301 1555 1555 2.18 LINK NE2 HIS A 187 MN MN A 301 1555 1555 2.12 LINK MN MN A 301 O2 AKG A 302 1555 1555 2.16 LINK MN MN A 301 O5 AKG A 302 1555 1555 2.47 LINK MN MN A 301 O HOH A 427 1555 1555 2.47 SITE 1 AC1 5 HIS A 131 ASP A 133 HIS A 187 AKG A 302 SITE 2 AC1 5 HOH A 427 SITE 1 AC2 16 LEU A 118 ASN A 120 TYR A 122 LEU A 128 SITE 2 AC2 16 HIS A 131 ASP A 133 HIS A 187 ILE A 189 SITE 3 AC2 16 ARG A 204 ASN A 206 THR A 208 ARG A 210 SITE 4 AC2 16 MN A 301 HOH A 403 HOH A 427 MA7 B 8 CRYST1 41.407 75.629 50.972 90.00 107.73 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.024151 0.000000 0.007721 0.00000 SCALE2 0.000000 0.013222 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020597 0.00000